Reuben and I heard from various sources that the Tsukiji fish market is the place to see in Tokyo, and after some googling, decided to go with a small tour provided by Mr. Naoto Nakamura(Link to tour page here).
The day started from the hotel at 3am, and we reached the designated meeting point at Tsukiji-Yon chome around 3.45am by taxi (the subway does not operate till 5.30am-ish). We were very fortunate as we were the only two people on the tour today, and had the full attention of Nakamura-san. The tour pretty much followed the schedule shown on the tour webpage, going through all the areas auctioning off the various seafood items. Nakamura-san knows Tsukiji Fish Market like the back of his hand, and it was more than well worth the initially thought to be pricey ¥7,500.
As many have said, the fish market is constantly busy at this time of the morning, and there are numerous motorised vehicles moving all around, so one has to be very careful walking about. Also, practical footwear is highly recommended as the ground is very slippery. Most of the regulars there do not mind tourists walking around and taking pictures, but there can be the odd one or two which displayed an immense amount of displeasure with us viewing and standing around the live tuna auction sites (which are technically out of bounds to non-workers).
After witnessing all the various auctions, ending with the live tuna one, Nakamura-san brought us to witness how middleman and master butcher Furukawa-san carved up his freshly purchased tuna and sold them on to restaurant buyers. Witnessing the carving up was a nice way to end his part of the tour, after which Reuben and I headed to the famous Sushi Daiwa for the mixed sushi set breakfast. The entire Tsukiji Fish Market was an amazing one, especially for photographers (high ISO, f/2.8, wide to normal angle lens), and while you could do it without a guide, you would also miss out on the wealth of information which no guide book could provide. Indeed the highlight of my Tokyo trip.