Best, is a very subjective term. I've owned both. All my life I've used Uniden and was familiar with their way of programming the scanner. A while ago, decided I wanted to try something different and try a Whistler, was put off by the steep learning curve of a new way to do things, and abandoned the idea. In my case,exposure to other radios in the professional realm, and their programming methods, equipped me with enough knowledge to figure out Whistler's way. Is easy really, you just have to keep an open mind and dig into it.
Eventually, got me a TRX-1 and liked it a lot. Immediately apparent to me, unlike the Uniden, the TRX-1 would break squelch a couple of seconds faster. From reading the forums here and there, apparently this is a bug with the Uniden.
I liked that on the Whistler, when telling the scanner what to scan, I did not have to remember quick key numbers as in the Uniden. You look at the scan lists available and choose what to scan (that is, if you taken the time and labeled each scan list with something meaningful to you) but, IMO by far, way better than coming up with a numbering scheme and mind trick to to remember what number you used to what you wanted to scan.
The Whistler can record on a per talk group basis, but have no easy way to enable this via front panel keys (is easier to do it via software). On the Uniden is just a matter of hitting a couple of keys and have it record everything right away. Oh, and the Uniden also has a replay key that you can hit and immediately hear something you didn't hear or understood, right away. On the Whistler, you have to get into the menu. It takes a little longer but is even more rewarding because you can choose exactly what you want to hear. You can listen to each recording individually or tell the scanner to start playing continuously at any point, say you have 10 recordings and you want to start listening in on from recording number 5 and the radio will play all files from there on. It can still be done with the Uniden but it takes a bit more button pressing.
You really have your work cut out for you, each radio has their own weaknesses and strengths. I suggest you start with what's more familiar to you and stick with that.