It depends. From a reputable source like MGM (who has AMAZING customer service!) I would be fine buying online. If, however, you are having to pay a lot for shipping, then you are better off in store if you are lucky to live in a place where they sell the uke you want in retail. One other factor, if the grain of the wood matters to you, perhaps you are better off in store because then you can see the actual ukulele you will be getting.
When I bought my Kanile'a there were two of the same model, but I didn't like the grain of the wood on the other. If I had bought it online, I would not have necessarily seen the exact ukulele I was getting, and I wouldn't have liked it with the blonde streak down the middle.