Have you tried printing it. Sometimes, Acrobat Reader does not display transparency well on the screen, but the pdf prints fine. If your output target is print, you don't have to worry about what it looks like on screen.
If you're on a Mac, try looking at the pdf in Preview. If you have Acrobat Pro, try looking at the PDF in that rather than Reader. If you have Acrobat Distiller, try printing an Adobe postscript file (or saving an eps file) and distilling that - set to press quality.
If you didn't create the gradient in Indesign, but imported another graphic format, make sure that its settings are ok. If it's a tiff, you might try removing any compression.
Youcan also try selcting Press from the PDF presets. After you click the Save and get the setting window go to Compression. You can set color downsampling to, let's say, 600, and set image compression to None. I'm assuming that, in the Image compression, you set the quality to maximum.