I think the big problem is you started to early (we are all impatient this time of year
) but otherwise, your plants look good. Tomatoes are hot weather plants - too cold or to damp, they pout and mildew. A fan to keep the air moving will help with mildew and make their stems sturdier. More light will also help.
What they need are larger pots. A pot big and deep enough to bury the entire stem, all but the leaves. You can pull them out of the cups they are in, place them at the bottom of at least a 1 gallon nursery pot (2 or 3 gallon if you have the space) and fill the pot with soil.
Next year, start your tomato plants about 4 weeks before the date you expect to plant them out. You are in zone 4a - your start date should be about now to be planted out at the beginning of June. (Just a guess. Any zone 4a people reading this thread?)