Phong Q. Nguyen, one of the main researchers on attacks on NTRU, uses Victor Shoup's NTL library, which contains an implementation of the LLL algorithm. That's C++, not Java; but this is the kind of number crunching job where the extra efficiency of low-level languages like C++ is handy. 95% of a given application code is not time-critical, and 95% of the remaining 5% is I/O bound (network I/O, disk I/O, RAM bus I/O maybe). Most hardcore crypto jobs (in particular attacks which need a lot of muscle) live in the 0.025% of code where everything happens in CPU L1 cache, and at that place properly optimized C or C++ code is typically 2 to 4 times faster than properly optimized Java code.
Anyway, to understand attacks on NTRU you will need to grasp some rather intricate mathematics, at which point something as trivial as a change of programming language should not bother you.
A good starting point for attacking a cryptosystem is to actually implement it yourself -- having your own implementation is handy if you want to print intermediate values or similar things, but the main reason is pedagogical: the process of implementing the algorithm is what makes you understand how it works, down to its fine details. Reusing existing code will deprive you of all this learning.
(Yes, I wrote that C++ is "low-level". Sue me.)