Low frequency noise (single Hertz and sub-Hertz) are frequently the
biggest pains on higher floors (swaying buildings) since damped tables and
active damping systems aren't that good at those frequencies.  
That said, I used to do Confocal on the 6th floor of an old shaky building
by a subway line (Columbia U) and now at the ground floor of a state-of-the
art Center (Harvard) and can say with some confidence that Confocal, two
photon, widefield, and other live imaging will not be affected much by being
on a higher floor.  However, for more sophisticated things (my Coherent
Synchrolock for CARS microscopy) and for metrology I would be a little
hesitant about a higher floor, that's why I can't speak much about
super-resolution.  Try to avoid long path lengths and have lasers as close
to the microscopes as possible.  Good temperature and humidity control are
more important along with clean air.  Unless you plan to do some very
sophisticated metrology, you should be ok with good optical tables.