There is a discussion on Boston.com today about where you can find the best local bagels. My personal local favorite is Finagle A Bagel, where I greatly enjoy their Wild Berry and Chocolate Chip bagels. Folks who like traditional bagels (plain, sesame, salt, etc.) will also be satisfied here.
Another great spot for traditional bagels and kosher sweet tooth satisfaction is Kupel's Bakery in Brookline.
Read the discussion here.