Funnily enough, medieval Bavaria is my jam.

First a view general ideas, that applied to all classes:

In general one would say, sauerkraut, bread, field beans, turnips and some sort of animal fat (depending on your region. Mostly pig's fat or in Alpine regions rarely butter/butter oil) were the back bones of nutrition. Especially the latter of course depending on the amounts one could afford. That means, unless there's a famine going on, or the person in question isn't able to spend enough on food in general, proteine, fat, vitamin c and carbs were available to most peasants.

They also occasionally could afford meat. Generally said, the less people there were, the more meat they consumed and the other way around. So during the population growth in 12th/13th century, meat consumption dropped and the mild climate allowed for more crops to be grown and people to be fed, but overall, they ate less meat. This also correlates with the warmer temperatures that made other, cheaper foods available for a longer period during the year.

When population dropped or a bad year destroyed the crops, especially during the start of the little ice age in 14th century, meat consumption rose, because there was less demand and prices dropped or people would kill cattle they couldn't feed anymore. Of course, people who couldn't afford meat at all would starve, which was a rare threat to nobility, unless impoverished. The usual meat was pork. Beef or veal was not that desired, because it's comparatively lean. The goal of a good medieval diet was to eat as much fat as possible.

For most peasants meat was reserved for celebrations, holidays and/or winter, when it was the most potent source of sustenance. Fowl and eggs were fairly common and expensive if not grown in the peasant's own home, venison was not legally available for peasants. They sometimes stole it, of course and at least in Bavaria it seems, that the punishments weren't that often imposed on peasants, but more often on clergy and Ministerials (it's basically "unfree nobles"). People could also catch fish and collect berries/mushrooms/roots in the forests, too.

Also fruit and vegetables would be available from spring to autumn, but if not pickled/dried, there wasn't much left during the winter. This meant, that during that time, not only was the population more vulnerable to starvation but also considerably low on vitamines.

Christian holidays sometimes gave lower classes access to higher quality food, because rich citizens or gentry would donate food.

Gentry had mostly two advantages, one being that they could afford more food, even when it was scarce, second that they were able to eat more meat more often. There was no way for them to buy fresh vegetables in winter though, and besides containing more meat a lot of "fancy food" was not marked by its nutritional superiority but by the expensive spices used in it. They sometimes could afford imported citrus fruit, figs or dates in winter, but not so frequently it would make a real difference.

They had a huge advantage when it comes to peasants with little, dependent farms who had to buy a lot of food, but not that big advantages when compared to peasants who owned bigger farms and were more self-sufficient.

When it comes to physical activity I don't think, gentry had a considerable advantage, since for most of them their job involved getting around a lot and that was a lot of hard work at the time.

In conclusion, there were a lot more malnourished peasants, than gentry. But there were, at least periodically, peasants as well nourished as them. If they were lucky enough to go through good times during adolescence it is fairly likely they'd be about the same size. Also, during good times, they were not that much smaller, than we are today, actually.

Could you please specify in which part of the world?

I guess you want to know about Europe, but even there's a huge difference in which part you lived (e.g. in the Mediterranean or in northern France)