17,000 is what the police announced, 200,000 is what TBS TV News said, supposedly quoting the organizers.
The photo below is taken from the helicopter (hired by the citizens' groups and IWJ) by the professional photographer Maki Ishii. It is the scene at one street corner. Protesters, many of whom had already learned from Twitter and other social media that there would be helicopters flown by the independent journalists and citizens groups, brought pen-lights and flash lights to wave at the helicopters.
Someone tweeted on this photograph, "At most 3,000. What's the big deal?"
"Hibi Zakkan" (daily random thoughts) blog (6/30/2012) has a summary of the Japanese media reports on the number of protesters at June 29's rally:
TBS TV: 200,000, quoting the organizers
Asahi Shinbun: 150,000 to 180,000 quoting the organizers, 17,000 quoting the police
Asahi TV (Hodo Station): 40,000 to 50,000
NHK: "More than the last time"
The Metropolitan Police: 17,000
Mainichi: quoting both the organizers (150,000) and the police (17,000)
Yomiuri: (there is no article)
Many news outlets quote Prime Minister Noda as he left the Prime Minister's Official Residence as the protest was going on around it. According to Jiji Tsushin, PM Noda said:
"Yes it is a big sound."
Here's another photo taken by a reporter from the Japan Communist Party newspaper:
As far as the police is concerned, it was a 17,000-strong protest overall.