does cry has two syllables?

No.

then does story has two syllables

Yes. STO RY has two syllables.

You can tell by its entry in a dictionary -- in print or online.

For example: sto·ry (2 syllables)
http://www.answers.com/story

Other examples:
http://www.answers.com/incredible
in·cred·i·ble (4 syllables)

http://www.answers.com/because
be·cause (2 syllables)

http://www.answers.com/interest
in·ter·est (3 syllables)

But if you look up "cry" there will be no dots separating the syllables -- because there is only one syllable.