You might look at JTB Japanican; they are the largest and reliable.
However, if you can search things through Internet, Japan does not require a guided tour for most people. Especially if you're on honeymoon, you would probably prefer to travel individually.
1. Get an open jaw ticket arriving at Narita or Haneda in Tokyo, and departing from Kansai International Airport in Osaka. Unfortunately, US based air companies currently have worse services than most airlines in the world, so I would recommend avoiding them if you are on a honeymoon.
2. Consider Japanican's Shinkansen e-voucher for Tokyo-Kyoto long distance travel, or standard JR Pass.
3. Consider some extra places to visit apart from Tokyo and Kyoto, like Takayama and Shirakawa-Go; Hiroshima and Miyajima, if you are going to get JR Pass.
4. Browse JNTO, Japan-Guide website, or English pages of major tourist attractions throughout Japan, for places you'd like to visit. Tripadvisor review pages can help too.
5. Consider hotel booking through Rakuten, Jalan, and Japanican hotel booking sites. Tokyo and Kyoto requires at least 2-3 days (Kyoto shouldbe a better place for honeymoon). Visit Nara for a day while you are in Kyoto.
Congratulations on your wedding!
Edited: 12:11 am, July 02, 2012