Both the Hilton Bonnet Creek and Waldorf Astoria are in the Bonnet Creek Area, near the popular Wyndham Bonnet Creek, but in no way associated.
Their bus service is very nice and contracted through Mears Transportation. Only the Hilton and Waldorf share the bus. The bus schedule is available in the lobby, and depending on the season the buses run every 30 minutes to an hour. There is typically a different bus for different parks (ie. One buss for Magic Kingdom, a shared bus for AK/DS, etc). We found the bus service pretty good, although they did leave us stranded at DTD one night in 30 degree weather, but that was right after the resorts opened and there seemed to be a lot of issues still being worked out.
We have stayed at the Hilton BC, but not the Waldorf. The two hotels are both less than 2 years old and are actually connected via a connection / meeting center. All amenities are shared, in other words guests at either hotel have access to all the facilities at the other (pools, etc.).
My thoughts are that the Hilton is the more "fun" of the two. Good service, pool with lazy river / slide, more casual restaurants on that side. The Waldorf is more "sophisticated". Slightly nicer rooms (from what I have seen), slightly better service, and a more tranquil, adult-style pool. The price difference between the two can be significant.
You really can't go wrong with either.