I'm wanting to do a little bit of 3D modelling mostly props for maps in the Unreal engine and Source engine. However, I would also like to take it a bit further and maybe try animated models at some point in the future mostly for a hobby but who knows where it might take me. I would say that I'm an above average map creator but I'm currently uncomfortable with creating 3D models.

I'm trying to decide the best tool to start learning with. I keep hearing about 3DS Max and Maya all the time but even with searching the differences between the two seem very hazy and I haven't really found a solid answer to which one would be best for me. I was hoping I could receive some advice here to help me decide which tool to begin with.

Thanks for any help.

Blender has its pitfalls imho but considering that it's free it is an awesome piece of software and I use it myself. I find it very hard to go away from it though and learn something more established. If you plan to ever do this professionally (as in job not hobby - not implying blender could not get you professional quality results) I'd go for something commercial.
Also not very widespread as far as I know is Modo, but I heard good things about it and afaik ID Software used if for Rage.

I'd heard of Blender before but haven't really looked into it until now. Some of those renders look very impressive. Why is a tool like Blender not used professionally? What sort of limitations should I be aware of?

The documentation is... less than optimal. The website/wiki can be confusing. Feature sets are not exactly stable (new features require code changes that sometimes break old scripts or features that existed in past versions are lost). Overall stability varies between versions.
The 3d industry was using commercial programs ever since because they existed long before blender was usable (I remember a time where it didn't have an undo function yet). When and why should they suddenly decide "hey, let's all throw our years of experience with commercial software xyz into the bins and start learning this badly documented free open source tool."?
Not very likely I'd say...
This might change over time with people getting started in the 3D industry as freelancers or small startups that start out with blender knowledge instead of commercial app knowledge. To people just wanting to learn 3D stuff for themselves Blender is very attractive since it's free and has a growing feature set.

I recommend blender, even though it can be challenging due to some of the aspects which are less automated as maya/3dmax. It is terrific for mechanical and prototype models. Even can be used for 3D printing and real rapid prototyping.

I would recommend sculptris for organic, it has a built in texturing tool which is brilliant in combination with Photoshop for finalization.

I hope this was helpful and good luck!