whatever parenthesis you open you have to close again, regardless of what you write inbetween, therefore (see Figure 4.2c)) is correct

Alternativley, you could used angled (aka square) brackets: [like this c)]. It's not as punctuationally correct, but I think it's at times easier on the reader.

I would omit the parenthesis after the figure number. When referring to a figure in the text, it is common to write "Fig. 4.2c", not "4.2c)". (See e.g. http://www.edpsciences.fr/docinfos/AA/instruc... or http://www.journals.uchicago.edu/ApJ/instruct.html)