These are fantastic and fascinating questions, but you're right that there's going to be quite a lot of variation both in time and in space throughout the medieval period. As a result, the following answer will not only be quite general, but will also really only be applicable to the 'core' of the medieval period and of Europe: i.e. France, Germany, Northern Italy and Southern England, c. 950-1350. Outside of these places and this period, the variations get even bigger and more significant, and I don't really know enough about them to answer coherently.

The first thing to note is that the medieval conception of wealth would have been quite different from ours. We tend to see wealth as correlating to our bank balance, but the medieval equivalent measure of wealth wasn't how many pounds of gold you had stashed in your dungeon. The point of being wealthy in the middle ages was to be able to flaunt it, by having an impressive home, luxurious things and an expansive entourage. Many of these things could be acquired without resource to cold, hard cash, through gifts, food and received obligations. In simple terms, if your peasants built your castle and provided enough food to feed your posse of knights, then you could be rich without having any money at all.

In reality, however, cash was an important part of the economy and became increasingly so as the middle ages progressed. Lords acquired their cash in three basic ways. The first two revolved around the productive capacities of the lord's estate. The classic 'bi-partite' estate was divided into the lord's demense (pronounced like 'domain') and the land he rented out to peasants. The demesne was farmed two groups of people. The first were the peasantry to whom to lord had rented out parts of his land. They were obligated to provide a set amount of labour to the demense each week/year, depending on the 'rental agreement' (rental agreement is an obvious anachronism, but I use it to try to get across the fluid and circumstantial nature of a lord's power of his tenants. These agreements were usually (but not always) unwritten and based on custom, and tended to be very conservative, rarely changing with the economic circumstances. One peasant might be far less 'oppressed' or owe far less rent and service to the lord than his neighbour, based on whatever circumstances had led his great-great-grandfather to first come under the domination of the lord's great-great-grandfather.) The 'corvée' labour of peasants on the demense lands was far more common in England than on the continent and persisted there longer too. The other form of labour on the demesne was in the form of unfree workers (essentially slaves) belonging to the lord or day labourers (paid at the end of each day). The produce of the demense was intended primarily to feed the lord and his household, but surplus could be, and frequently was, sold for profit. This is the first source of lordly cash. It should be noted that the demense economy seems to have been less important to the medieval rural economy than historians have estimated in the past, particularly outside of England. The idea that it was the basis for a totally self-sufficient estate, divorced from local markets and exchange, is also no longer tenable.

The second supply of cash came from the rents of the peasants to whom the lord rented out the rest of his land. As I said, these rents could include labour services, and were certainly often paid in kind, but the vast majority (for which we have records in any case) were paid in cash, certainly on the continent. The fact that peasant cultivators paid in cash is strong evidence for the existence of local markets for crops and for other basic agricultural produce. It is important to emphasise that these exchanges were local and small-scale, for the most part, with surplus food being sold to other peasants and to local non-cultivators (clergy, trade- and craftspeople,knights etc.). These are the exact same small-scale markets that the lords would have been selling their demense surplus in.

Over the course of the central middle ages, we can see a trend of more and more production being geared specifically for the market, rather than simply surplus being sold there. This goes hand-in-hand with the development of wider, regional and supra-regional markets and the increasingly rapid urban development across Europe. The medieval cash-crops that were being invested in specifically with an eye for the market included vines/wine (in Loire valley, Tuscany and elsewhere), salt (French Atlantic coast, Eastern Europe), olives/olive oil (Italy), wood (Champagne) and sheep/wool (Northern England and Spain). We can see both peasant cultivators and lords investing in these types of markets, often together, although by the 14th century there is more and more dominance by bigger producers (such as the Cistercian wool production machine).

The final, and seemingly most effective, way by which lords extracted wealth from their lands was through their various rights over the land which were extra-agricultural (i.e. didn't relate directly to crops and production). The medieval rural economy was not only just fields - meadows and hills for pasturing animals, woods and forest for wild food and firewood, rivers and streams for fish and power, mineral deposits for silver, iron: all produced wealth. Although lords could (and sometimes did) run these themselves for profit or subsistence (like the demense), by far the most common option was to use them to generate income directly, by charging people (primarily the local peasant population) to use them. This was then, in essence, an extra form of rent upon the peasantry. Lords increasingly expanded this economic domination by imposing other charges on the local populations: charges to use the mill, tolls on bridges and roads, levys on local markets and the rights to the proceeds of justice (i.e. all fines paid for criminal offenses went to the lord). The church, itself the biggest landlord in Western Europe, also heaped on the expenses, with yearly tithes, burial dues, baptismal dues and other obligations on the parishioners (which were also sometimes paid to the local lord, not the church). The nature and novelty, as well as the effect, of these 'seigneurial dues', as these bundles of heterogeneous rights are called, are heavily debated amongst historians, but they are rarely to be seen in documentation before the end of the tenth-century and they seem to have coincided with a big increase in the wealth of the lordly class (including the church) and to the widening of the gap between the richest peasants and the poorest nobles. By the beginning of the 14th century though, these rights were common and institutionalized, and beginning to be challenged by the growth of towns and the demographic collapses of the Great Famine and the Black Death.

I realise the post is slightly rambling and not particularly coherent, but I hope you'll forgive it that and that it still somehow managed to answer your question. My excuse for its nature is that the scholarship on this field has been pretty much neglected for the past 30 years, in which time lots of problems have emerged, with no real answers. The place of small local markets and of the impact and significance of seigneurial dues in the economy are two topics in particular which are grossly understudied. As a result, I can't really recommend any particular single book to read further on this topic, but if there's anything in particular you'd like to know more about I'll do my best to expand on it/provide further reading.

One important point is that we tend to focus on the wealth in and income from ownership and feudal entitlement to land because that was the form of wealth and income that the political and military elite had, and the political and military elite are those upon whom history concentrates.

Manufacturing, construction, trade and finance were substantial sources of wealth, especially as crafts evolved into outright industries, but their owners / practitioners are obscure to history except in the relatively rare cases (as in certain Italian city states) where that slice of rich people became the military and political elite.