I'm an assistant professor in my fifth year and have decided to go on the job market this year. Obviously I prefer tenured positions to pre-tenure positions, but I'm interested in either one. Would it be weird to leave this ambiguous in a cover letter, that is, to simply say "I am applying for a position in your department" without specifying the rank? It seems to me that if I say I'm applying for an associate position, then some departments might say "oh, she's not ready for an associate position, too bad, we would have hired her at the assistant level", whereas, if I apply at the assistant level, I might be passing up opportunities for a tenured position.
I suspect this is one of these questions where there is no truly "correct answer" as you can't predict what's going on in any given search committee, but I think you're unlikely to do any damage by leaving it open. At least my understanding of these things is that a department would rather hire you w/o tenure (note that this is not quite the same as the associate/assistant distinction) as it is less of a headache with the administration; you'll get tenure if they really want you, and don't think they'll get you otherwise. I don't think it will matter much what you wrote in your cover letter. Concentrate on making them want you, and then worry about what they have to do to get you.