Booleans are great if you can get them to work. I don't really have any issues with them as I try to keep my geo as clean as possible.

As stated before do a clean up, but make sure you have the non-manifold option ticked otherwise it wont show you any of the issues (go into the option box).
Ensure the 2 pieces are intersecting and are complete bits of geo, no holes and no open ends etc...


Other than that you are left with a Poly Combine option and a bit of har work merging and deleteing. Kurt goes through this well in the Cartoon Dog Tutorial on this site.