I've run both and they both have good reasons to run.. Personally, more of a daily driver if it's a fox body 5 speed I'd say run the 3.55's as it still pulls hard on the street, don't have to shift out of first so quickly (and often if you get in stop and go traffic), and if you throw a little nitrous on it, it helps you on the top end.
If it's a 4.6 I don't think you can run enough gear LOL. higher the number (lower gears) the more fun the 4.6