Not sure of your price range, but I live in DC and lived in Baltimore for 4 years too. In Baltimore, I'd recommend the Hyatt in the Inner Harbor. It's a gorgeous hotel and in a good location. For some reason my mind is completely blank on other hotels-there was an Omni but it has a new name now. Brookfield Suites is not that great so I'd avoid that if possible-not horrible, but the a/c broke when my family was staying there in late May-very hot room. Stay in the Inner Harbor area and you'll be okay, but try not to stray far from there cause it gets sketchy fast in Baltimore.
DC, I also like that Embassy Suites in Chevy Chase-I worked in that building before my daughter was born and I live in downtown DC and it was a very quick, easy commute. The metro ride from Friendship Heights (right below your hotel) to Dupont Circle is only 10 minutes-and even shorter to the zoo if you're going there since I see you've got kids. (I don't really recommend the zoo cause it's really not that great, but kids like it, at least mine does.) Downtown there's a JW Marriott at Metro Center that is very nice, in the Dupont/West End/Foggy Bottom area (where I live and love cause there is so much nearby-it's a short walk to Georgetown, quick walk or metro to the monuments) there's a Marriott (which is okay, nothing spectacular), the M Street hotel (similar to Marriott), a Fairmont, Ritz-Carlton (though of course that one is so expensive, but again, not sure of your price range and it's in the area so I thought I'd mention it anyway). Then in Crystal City, VA there are a ton more that are less expensive (Hampton Inn, Hyatt, Marriott (I think Courtyard)) and then some in Rosslyn too (Holiday Inn Key Bridge). If you stay in DC itself, I wouldn't stay anywhere other that NW DC cause the other quadrants can be sketchy.