The ceviche at Tico is the best I've had in the city (and I'm not the biggest fan of Tico overall). The scallop ceviche is truly, truly special, but all the versions I've had there are excellent. Good balance of chili, citrus acidity, and fat. Someone knows what they're doing.
I don't know about "best", but I'm fond of the ceviches at Rincon Limeño, a Peruvian place in Eastie. I've had some nice, fancier versions at Rendezvous in Central Square.
The crudos (crudi, I suppose) at places like Neptune Oyster, Erbaluce, Coppa, and Toro are also worth checking out.