Full Moon on that list is the first thing I was going to recommend. It's totally geared to be kid friendly, with crayons on tables, buckets of toys, and a play area in the back. It sounds like your kids are too old for those, but it's still a very friendly atmosphere where you'll feel like the norm instead of the exception at a restaurant.
What sets it apart from the traditional family go-to restaurants is that the grown-up food is fantastic. It's worth going to just for the food. Mostly Mediterranean skewed food, but there's lots of good options. My favorite dishes include the Carne Asada (HUGE chunk of meat), the mussels & chorizo stew, and the steak with bleu cheese butter.
The reason I asked if the kids were geeky is because you're not too far from the Miracle of Science bar/grill. It's not specifically kid oriented, but it has burgers, quesadillas, chicken skewers, and other kid friendly options. What makes it fun is that it's science-themed (it's next to MIT), with chemistry lab tables and the menu laid out like a periodic table (with common themes in vertical groups, naturally). It's right next to the MIT Museum, which is small but fun and also worth a look.
You'll find a lot of food options on Charles Street right next to you; definitely worth walking down just to see if anything catches your eye.
Another restaurant to consider is Dick's Last Resort, which the kids could get a kick out of. It's a gimmick restaurant but the food is good. The idea is that the waiters are intentionally rude and brusque with the customers, also insulting them and writing belittling messages on paper hats they're made to wear. I've only been a few times, but it seems the waitstaff is good about tuning the level of crassness to the group, so unless I'm horribly mistaken it's totally kid friendly.