In Colonial North America (my area of specialty), the "best" places in terms of climate, disease, and agriculture for the average settler would the colonies of Pennsylvania, Maryland, and the Jerseys. All three had very fertile soils, mild winters, and an absence of the oppressive swamplands and humidity of places to the south.

The so-called backcountry of Virginia and the Carolinas was also free of the humidity and possessed fertile valleys that were attractive to new migrants.

Early on, the lower Connecticut River valley and Long Island were also attractive options for their access to port towns and much better soils and climates than those found in Massachusetts and New Hampshire.

There's no one answer to your question. The ideal location for any settlement is going to depend on exactly what the goals of the colonial power are and what resources they're attempting to extract from the area. There were a few key ingredients that colonial powers looked for in official expeditions though. First and foremost was simply the ability to reach the settlement. Areas that were difficult to reach were often largely ignored by colonial powers until transcontinental trade networks began to appear. The modern cities of Calgary, Hermosillo, and Phoenix are all examples of this. The most important criterion for "reachability" in the Age of Exploration was the ability to sail there. As it happens, the Americas have a number of absolutely spectacular harbors, especially at San Francisco, Rio de Janeiro, and Havana. These three harbors are each easily among the greatest in the world. They all were a tremendously important resource in the evolution of their respective settlements. The harbors at New York, Boston, and Veracruz were similarly important in the colonial era, but struggle to accommodate modern demands.

Climate is also an important criterion, as you pointed out. Of the three great harbors I mentioned, all have extraordinarily mild climates. Even more amazingly, two of these mild-climate areas with spectacular harbors are all nearby to some of greatest agricultural land on earth. San Francisco guards the entrance to the San Joaquin river, which flows out of Central Valley through Stockton. Today the US is perhaps the most agriculturally productive country on earth. Central Valley produces 25% of the food eaten in the US, but contains less than 1% of its farmland.

Rio de Janeiro is only marginally inferior. In agricultural terms, Brazil is nothing less than an international heavyweight. The Southeastern region where Rio is located produces more than 60% of Brazil's agriculture on its own.

The absolute absurdity of these cities doesn't even stop there. Just offshore of Rio sit some of the largest petroleum reserves in the Western hemisphere. Within the San Joaquin valley sit even more petroleum reserves, enough to sustain global consumption for upwards of a year.

It's no coincidence that both of these are thriving modern cities with massive populations and hugely important economies. Almost any large city would be a good candidate for colonization given the reasons that historically led to their development. Calgary had the confluence of the Elbow and Bow rivers. New York has a fantastic low-draft harbor. London has the Thames. The Bay area and Southeast Brazil are nearly unique over the entire world in simply how many spectacular features they have that make them enormously productive regions.