You should ask this question on
www.jeepsunlimited.com.
I would NOT go with JC Whitney. You want to make sure you get a BestTop brand top, they are the best. If you can afford the extra money, the "sailcloth" top is definitely worth it - it is a thicker material, much quieter, and generally nicer in general. I have a besttop sailcloth replace a top on my 99 Wrangler and it is GREAT. The tinted windows are cool, too. I think a fully decked out top (sailcloth, tinted windows) will cost you in the $580-620 range. The regular besttop replace a top will probably be closer to $450. If the jeep sees the highway a lot, definitely consider sailcloth.
As for good online vendors, try 4 wheel drive hardware or quadratec, either are good. You have to compare not only the cost of the item, but also cost of shipping, and sometimes the different online vendors do weird promotions, like free shipping or 10% off all tops, etc. Apparently the besttop prices are semi-fixed, but they can do "specials" to get around the price fixing.
A new soft top is a great thing to add, they aren't really _that_ expensive and the difference in appearance is great.
Any specific questions, feel free to email me.. (I'm on my 3rd wrangler)