The basic point as so correctly noted by previous posters is that both companies make really awesome knives. I have both, I use both, I love both, I will continue to be unable to stop purchasing more of both
The Beckers will cost less, but that's mostly because off the shelf they come with plastic handles and very simple sheaths. Most people are okay with the handles; many people HATE the sheaths (except the new Shorts line sheaths; very nice). The ESEE knives cost quite a bit more, but most come with micarta handles and pretty good plastic sheaths. The knives cost basically the same if you buy micarta handles and a kydex sheath for your Becker. ESEE has modular sheath systems that are really cool.
Both lines of knives are really well-made, absolutely dependable, and fun to use.
Both lines of knives are infinitely modifiable.
Both companies are headed up by designer/manufacturer teams that you can feel good about giving your money to.
Both lines are made in the USA.
Becker/KA-BAR and ESEE have great warranties... ESEE's is no-questions-asked, KA-BAR isn't quite there but still better than most.
Both lines of knives are well-designed. Most people tend to like the Becker handle shapes better, me included. I personally like the Becker pommel design much, much better than the ESEE's. I like the ESEE neck knives more, the Becker mid-size and large knives more.
Becker knives come black. ESEE sells a wide variety of colors, some of them awesomely ugly (I say this as a compliment).
There are a few niches only filled by one company or the other. ESEE makes a standard long machete that right now you can't buy a comparable Becker. Becker makes a pure chopper (the Machax, which in theory at least will be released any day now) that doesn't really have an ESEE equivalent (the ESEE Junglas is really a Becker BK9 analog) along with a demolition knife (the Bk3) which doesn't appear in the ESEE lineup. Note that Becker has several knives in the line that as of now have been discontinued and can only be found on Ebay for a lot of money.
Hope that helps.