I've ordered from both. Great customer service from both. Connecting Threads produces their own fabrics, Whittles has different manufacturers.
I like the batiks from CT, have ordered and will again. Their blenders (Mirage) are great and you can't beat the prices. If you don't like the krinkle look in you quilts, I would wash all fabrics before using to allow for shrinkage, it seems to shrink a little more than some. I would suggest ordering a charm pack of the fabric line that you are interested in using from CT before you order your whole quilt, just to be sure you like the print. They have great prices on books and patterns most of the time.
If you are lucky enough to find a fabric that you like on Whittles' web site, go for it. I've never had a problem with any fabric and the customer service is tops. They will send you a sample if you are uncertain. Their web site is very easy to understand.