Your best bet is probably to grab a good c book (K&R: The C Progranmming language) a cup of tea and start translating! I would be skeptical about trusting a translation program, more often then not the best translator is yourself! If you do this one, then its done and you don't need to keep re-doing it. There might be some complications if the library is open source, you'll need to check the licence carefully about this. Another point to consider is that there is always going to be some element of risk and potential error in the translation, therefore it might be necessary to consider writing some tests to ensure that the translation is correct.
Are there no JAVA equivelent Math functions?
As you yourself comment the JNI way is possible, as for a c compiler you could probably use 'Bloodshead Dev-c++' might work, but it is a lot of effort for ~5000 lines.