Dinner w. a Toddler near Boston Common
I took my son (now almost 5) every where in Boston for dinner with no issues. The key is to eat early(between 5:30 and 6:30) so you are done before the anti-kids contingent show up. (and I am one of those anti-kids people when I book a babysitter and make a reservation for 8:00 and find myself seated next to a table with kids.) If you follow that rule I don't know a single place that would be off limits.
I have also found the kid friendliest is anywhere in Chinatown. My son at 18 months loved spicy dumplings, chicken feet and sesame noodles. The staff loved his adventurous appetite and catered directly to him making for a great time for mom and dad too.
I would second this - we have a soon-to-be 3-year-old and we have taken her everywhere with us, just early.
I'd recommend bringing your own booster/high chair seat w/you, though. This is OT, but we had the Fisher Price one that straps to a chair easily and has a snap-on tray. You can use/or not depending on how old and facile w/table eating your kid is. Saved us many a time and it's lightweight. Bon appetit!