Coppa Enoteca does a spaghetti alla carbonara with sea urchin, bacon and egg that is really nice.
Toro usually has sea urchin in a couple of tapas, like erizos, a little stew of uni, crab, and Maine lobster. They used to serve this in half a sea urchin shell with the spines blunted, very cool, but I don't think they do that anymore.
Both Coppa and Toro (which have the same exec chef) have done a bocadillo, a little pressed sandwich of uni and something else rich and creamy (marrow, miso butter, like that), but I don't see them on either current menu.
Clio has a long-running cassolette of sea urchin and Maine lobster on its app menu.
O Ya uses sea urchin to good effect in several of its nigiri, sashimi, and noodle dishes.
253 Shawmut Ave, Boston, MA 02118