Since you didn't specify cuisine, my suggestions will be based on the take-out experience (ie. packaging, efficiency, and of course taste).
-Oyster Boy - you can get pre-shucked oyster with condiments!
-Libretto - always friendly and fast (if you call ahead)
-Delux - Cuban Sandwich + Milk & Cookie, always fast and friendly.
-Alex Rei dos Leitoes - great 1/2 chicken dinner, phenomenal price, lightening speed.
-Feel Good Guru - slow service, good feel good vegan food, but you can bring in your own container, which for me, is always the best way to do carry out on my bike.
-County General's burger is always good, but like all fries, they don't travel well.
-Fresh - over-priced salads, but a safe bet.
-Clafouti's - Great croissant sandwiches.
I found all of the above to do a superb job in packaging (so that nothing leaks) and taking pick up orders over the phone.