Short Answer
I'd go with Java Bytecode.
Long Answer
The thing is, the higher-level the language you compile to,
- The slower and more cumbersome the compilation process is
- The more flexibility you get
For instance, if you compile to C, you can then get a lot of possible backends for C compilers - you can generate Java Bytecode, LLVM IR, asm for many architectures, etc., but you basically compile twice. If you choose LLVM IR you're already halfway to compiling to asm (parsing LLVM IR is far faster than parsing a language such as C), but you'll have a very hard time getting Java Bytecode from that. Both intermediate languages can compile to native, though.
I think compiling to some intermediate representation is preferable to compiling to a general-purpose programming language. Between LLVM IR and Java Bytecode I'd go with Java Bytecode - even though I personally like LLVM IR better - because you wrote that you basically want both, and while you can sort of convert Java Bytecode to LLVM IR, the other direction is very difficult.
The only remaining difficulty is translating your language to Java Bytecode. This related question about tools that can make it easier might help.
Finally, another advantage of Java Bytecode is that it'll play well with your interpreter, effectively allowing you to easily generate a hotspot-like JITter (or even a trace compiler).