Since I am Japanese who can read and write in Japanese, I researched about it in Japanese web site.
I found the record about this B-29 serial number 44-69742 shot down by AA-gun and crashed down in Tokyo Bay on 5/24/1945.
This airplane was belonged to 20th Bomb Squadron, 73rd Air Division, 500th Bombardment Groups, 882nd Bombardment Squadrons.
US made massive air raid over Tokyo area on 5/24 through 5/25 with using over 500 of B-29s. (995 B-29s in 2 days)
On 5/24, 557 of B-29 joined the air raid and 69742 was one of them.
10 of them got shot down over Tokyo and 4 of them crashed into Tokyo Bay.
(7 more B-29 crashed down while returning to the base)
There were 4 survivors (on those crashed into ocean) and Lt William H McClure was one of them. They were taken to Eastern Gendarmerie headquarter as POW and released after the war.
10 other crew members of 69742 were all dead including your cousin 1Lt Leonard I Hughes (0-683454).
On same day, 4 dead body (Unknown American soldier) were found at the shore near Yokohama and buried at Kouen temple at Tsurumi, Yokohama-city.
Anyway, there were no report or website about B-29 wreck in Tokyo Bay.
Tokyo bay is very deep (about 230ft). So, once it sunk in the bottom of ocean and covered with mad/sludge, nobody can find it.
There were many B-29 shot down in Japan. And some of them has memorial monument.
The following pic is the memorial monument of #42-24826 "In the Mood" shot down on 5/25/1945 (the 2nd day of air raid).