NJPW and AJPW are still the best to watch today - AJPW took a turn for the worse after Misawa left and took half the roster to form NOAH, but while NOAH is not in good health today, AJPW has really improved a ton this past year or two, with guys like Suwama, Shuji Kondo, Takao Omori, Jun Akiyama, Kenny Omega, Hiroshi Yamato, etc, putting on some great matches. NJPW is doing well also and still the biggest company in Japan, although puroresu as a whole is down in popularity. Guys like Shinsuke Nakamura, Hiroshi Tanahashi, Tetsuya Naito, MVP, Minoru Suzuki, Prince Devitt are some of the best to keep an eye out for in NJPW.
If you're looking to watch some online, I've got a bunch of shows up on DailyMotion;
http://www.dailymotion.com/playlists/user/SenorLARIATO - I'd definitely recommend the
03/20 AJPW show, which was one of the best puro shows in years from top to bottom.
Yeah, and just had an awesome match against Mutoh. I'm loving his title run and the role he's playing as the returning AJPW veteran, now representing rival promotion NOAH.