What would the best tool to create a natural DSL in Java?

You might want to consider Xtext, which internally uses ANTLR and does some nice things like auto-generating an editor for your DSL.

Considering the complexity of lexing and parsing, I don't know if I'd want to code all that by hand. ANTLR isn't that hard to pickup and I think it is worthing looking into based on your problem. If you use a parse grammar to build and abstract syntax tree from the input, its pretty easy to then process that AST with a tree grammar. The tree grammar could easily handle executing the process you described.

You'll find ANTLR in many places including Eclipse, Groovy, and Grails for a start. The Definitive ANTLR Reference even makes it fairly straightforward to get up to speed on the basic fairly quickly.

I had a project that had to handle some user generated query text earlier this year. I started down a path to manually process it, but it quickly became overwhelming. I took a couple days to get up the speed on ANTLR and had an initial version of my grammar and processor running in a few days. Subsequent changes and adjustments to the requirements would have killed any custom version, but required relatively little effort to adjust once I had the ANTLR grammars up and running.

Good luck!