@jpaugh is right: Usually a seq is all that you need. Many clojure collection functions work on many different structures, including seqs. If you need other collection types, though, you can often use into:
(def java-array (long-array (range 3)))
(into () java-array) ;=> (2 1 0)
(into [] java-array) ;=> [0 1 2]
Note that using into to create a list reverses the input order.
One can often use Java arrays as if they were Clojure collections. I recommend just pretending that an array is a collection in some test code at a REPL, and see what happens. Usually it works. For example:
(nth java-array 1) ;=> 1
@jpaugh's answer provides another illustration.