Fiberglass has it pluses and minuses.
Most of the big vinyl detractors will invoke the "Green" argument that vinyl is toxic and blah, blah, blah.
Not to discount their position as there is some merit to every argument.
Fiberglass is not with its own environmental repercussions as well, however, back to the argument at hand.
John is dead on correct about the manufacturing and assembly requirements of fiberglass. There are more moving parts and fasteners and from that standpoint they would be more prone to leakage. I have not yet replaced a fiberglass window that leaked at the corner so I cannot speak specifically to the likelihood of that happening but it makes sense on paper.
Multiple chambers vs. not multiple chambers, that argument is kind of a wash in my book. Vinyl uses multiple thin chambers for structure and insulation where as fiberglass is typically a much thicker pultrusion and seems to have similar (not quite as good) thermal performance in the frame and sash sections.
Fiberglass will require more maintenance that the vinyl when it comes to up keep and painting so take that into consideration if you are not wanting to do anything for the long run of the windows.