I bought my molcajete at the Crate and Barrel downtown - it's not huge, but for $30, it holds enough salsa or guacamole for a small gathering.
As for ingredients/cooking utensils, there's a little storefront in Union Square, Allston called Mayfair Food that might be worth looking into. They have a lot of mexican/south american imports - sugars, grains, dried chilies, etc. and there's also a section for utensils. I've never purchased anything besides the ingredients, so I can't vouch for quality, but it's a possibility.