You could easily interline the X90 with any of the express buses that terminate on East 57th Street. In the AM, after a Manhattan bound express bus from Staten Island or a BM1-BM5 terminates along East 57th Street, continue along, left onto 1st Avenue, right onto 92nd Street and make the first pick up stop at York. In the PM, start a new bus as an X90 from the World Financial Center, then after it makes its last stop on 91st Street and York, send it around 1st Avenue to 92nd Street, back down York, right onto 57th Street and start it as a Staten Island or BM1-5 express bus.
I don't get what the issue is here. This is almost exactly like how they interlined the X29/X25. The northern terminal for the X90 and the SI and BM1-5 express buses are only two miles apart, which should take no longer than 10-15 minutes to go between.
If anything's unclear then tell me and I'll be more than happy to create a map for what I'm saying.