This is probably a better place to get the food and take it out. Really... it is a fish market and warehouse, so, you would expect that it would smell like... well... FISH. It does. They now have a dining area, that is really quite lovely. You order your food at the counter, and then seat yourself in the dining area. (No wait staff, per se, although there is a woman there who serves beer and wine only) There is a closed door, but everytime it was opened you would get a huge waft of those giant fish tanks. This is probably OK for most grown ups, but not for a 2 year old, who refused to eat her meal.
They have several options for kids, from a $3.99 kids menu (drink not included). Fish "hot dog," fish nuggets, hamburger, clam strips. All come with fries. Portions are generous for the kids, and also for the adults. Most of the menu is under $10. You pay more for the Lobster Rolls (which are excellent by the way.)
Both the retail shop and the sit down area for eating are wheelchair accessible. However, to go from one to the other, you do have to go outside because there are stairs in between the spaces. This might be uncomfortable on very cold, or rainy days.
So, my suggestion would be to go to Fish City--but eat off the premises if your little one is sensitive to smells!