Hi,
1. Web based is secured if you use HTTPS connections and faster according to your internet connection. It will neither take any additional installations nor client pc resources, and only run in a browser, so you can assume it is faster. But in 2013, user friendliness is bit of a problem.
2. VPN's are good, secured out of the box if you use a reliable product (Please check with your internet provider). You have to install the client and internet resources will be also used. But if your client hardware is strong and internet is good, this is a good option.
3. Remote desktop is secured upon the certicates that you obtain/create. In my experience, remote desktop is much more reliable and faster since it is native Microsoft. But other two solutions are either based on the VPN product you select or the browser you use. But if you are using RDP over the internet, then your internet speed is a concern too.
Hope it helps.