We didn't use a TA. I booked everything myself. I do a lot of travel for business, so I am very well versed in travel. That being said, you can easily do it yourself....but if it's not something you are comfortable with, definitely use a TA. I really wished we could have seen the Castle with snow on it!
Luckily, we were staying with friends at the Disney E-Village (Entertainment Village). Hotels are VERY expensive (ok, everything in Japan is expensive). If you want to stay around the resort, there are 3 or 4 hotels. Rooms are standard size. I would recommend the Hilton if you're staying there. There is bus service to the parks in very cool, "retro" looking buses. The resort is also at the Mahaima (I think) train station that will get you into Tokyo to explore.
As far as being safe to travel, I would have no problem doing it again. Japan is a very safe and friendly country. They may not be able to communicate verbally with you, but most people have studied english and can at least understand what you are asking. The one thing we learned while being there is simple. If in doubt...ask. We had our instructions from our friends on how to get a bus ticket to the e-village. We weren't quite clear on some of it. We asked as we got off the plane. Not only did the person try to explain it, they actually took us to baggage claim, waited for our luggage, took us to the bus ticket stand and waited with us until the bus came. They also gave us their phone number if we wanted a "guided tour" of Tokyo!!! We were told we could leave out wallet on a trash can in the train station and come back the next day to get it. It would still be there with all of the money in it!! It's an honor issue with the Japanese.
If you plan on doing a lot of exploring, get a rail-pass before you leave the US. They are not available in Japan. It's basically an unlimited use train ticket while you are in Japan. We knew we weren't going to be there that long, so we bought 1000yen ($10) tickets while we were there. When they run out, buy another one.
The best advice is stay as long as you can. See the parks and then explore. Also, if you see a lot of Americans at the Mahaima train station, they are more than likely cast members. Ask them for any tips. They are usually more than happy to share information.
I hope that helps...I can recommend a couple of travel books if you're interested.