TA won't reveal its ranking system but they look at a lot more than just the number of 4s and 5s or the percentage of recommend, although it seems those 2 factors do weigh very heavily for them.
They also, though, look at the overall credibility of an inn's reviews. For that, the number of high-profile reviews that link to your inn really matter. NY Times, for instance. Or Frommer's. If the inn that's ranked above you has a lot of travel reviews out there and you don't, they'll get a stronger rating on TA.
Still, if there's a disparity as strong as the one you're talking, it's worth having them take a look.