Booked for a day trip with the family
Meat sandwiches at Milk St for lunch, ducky tour for fun, and Taam China for dinner? Any other activity for a 2+5 year old?
Aquarium as mentioned above.
Boston Children's Museum and Museum of Science are both very enjoyable for those ages. If weather doesn't cooperate, you'll have good museum options. But if weather is nice, they'll probably enjoy the Public Garden, visiting the Make Way for Duckling statues and even doing the Swan Boats. You can do Duck Tours and Swan boats in the same day!
I'm a big fan of Taam China's General Gao's chicken. Their pupu platter is fun but sometimes the items are dried out. You'll be right across the street from mincha at Israel Bookstore 2PM. And right next door to Kupels, so you can try the frozen dough, whatever that is.