Here's the short version:
Whistler supports NXDN, Uniden currently does not (though it could be added in the future). If you need to monitor NXDN right now, Whistler is currently the only option.
Whistler and Uniden both support DMR, but Uniden charges $60 extra to enable DMR. Whistler includes DMR in the scanner price.
Uniden supports location-based scanning with GPS, which means you can travel anywhere in the USA or Canada (or anywhere else, if you program a Favorite List with location data) and always hear local traffic as you go without manually toggling things on and off. Whistler does not integrate GPS with their scanners; you always have to manually set your location.
The Uniden 536 has Wi-Fi, which allows you to stream audio and remote control the scanner with a computer, iPhone, or Android. This means you can physically locate the scanner close to where the coax enters the building, and still access it anywhere within Wi-Fi range.
ProScan is by far the best software option for computer remote access; it can be set up as a client to monitor and control the scanner, and also as a server to stream the scanner audio to multiple internet clients. The phone apps work, but are limited to connections on the same LAN, and are prone to audio buffering issues. They are more useful for remote control than listening IMO.
Neither Whistler or Uniden handle simulcast perfectly.
Uniden is somewhat better at handling interference from adjacent channels.