You could also adjust the topping lift slightly to raise the boom, or as described above modify the heigth of the boom or the mainsail, which would be drastic. Personally, I would not modify the boom or sail as this will negatively affect sailing performance.
Raising the boom will put excesive slack in the leech of the mainsail, & cause it to billow outwards, loosing efficiency. The best option is to reduce the heigth of the bimini frame, slightly until the boom clears it. Or as I mentioned before have some leather chafe strips sewn into the front of the bimini to reduce wear from abrasion. Or you can just live with it, but its the lil' things that don't work right that tend to drive me crazy after a while!