If I were you, I'd remove the ambiguities. You can often do that by using contextual information to determine which grammar rules actually trigger. For instance, in
C* X;
in C (not your language, but this is just to make a point), you can't tell if this is just a pointless multiplication (legal to write in C), or a declaration of a variable X of type "pointer to C". So, there are two valid (ambiguous) parses. But if you know that C is a type declaration (from some context, perhaps an earlier code declaration), you can hack the parser to kill off the inappropriate choices and end up with just the one "correct" parse, no ambiguities.
If you really don't have the context, then you likely need a GLR parser, which happily generate both parses in your final tree. I don't know of any available for Java.
Our DMS Software Reengineering Toolkit [not a Java-based product] has GLR parsing support, and we use that all the time to parse difficult languages with ambiguities. The way we handle the C example above is to produce both parses, because the GLR parser is happy to do this, and then if we have additional information (such as symbol table table), post-process the tree to remove the inappropriate parses.
DMS is designed to support the customized analysis and transformation of arbitrary languages, such as your query language, and makes it easy to define the grammar. Once you have a context-free grammar (ambiguities or not), DMS can parse code and you can decide what to do later.