The stack size, I understand, depends on the JVM you are using as well as the platform. If you are using the Sun JVM, you can use the -Xss and -XThreadStackSize parameters to set the stack size.
The preferred way to do recursion in Clojure though is to use loop/recur:
(defn fact [x]
(loop [n x f 1]
(if (= n 1)
f
(recur (dec n) (* f n)))))
Clojure will do tail-call optimization for this; that ensures that you'll never run into StackOverflowErrors.
Edit: For the record, here is a Clojure function that returns a lazy sequence of all the factorials:
(defn factorials []
(letfn [(factorial-seq [n fact]
(lazy-seq
(cons fact (factorial-seq (inc n) (* (inc n) fact)))))]
(factorial-seq 1 1)))
(take 5 (factorials)) ; will return (1 2 6 24 120)