The John Harvard's in Harvard Sq. is actually pretty decent-- the food is quintessential pub grub. Besides their regular lineup, there are quite a few seasonal/specialty brews the brewer puts out on a regular basis. I haven't been in about a week, but last time I was there they had a 12% wheat wine and their demon double pale ale on. Both were very good. Their RIS called midwinter's is also quite good. So is their saison.
As far as brewpubs in the Boston area go, this is second best to Cambridge Brewing Co.