Usually the kayak and the dinghy are kept with the boat. You use one or the other but not both. Since he has his bag it doesn’t seem like he was out kayaking but used the kayak to get to the boat. The ladder is to get up to the big boat.
It actually look like the last time he anchored he used the kayak to get to shore so was just using it to get back out.
I went to this article and it looks like he is the lone person boarding the zodiac, which is just off shore.
So he probably went for a bit kayaking or is just coming from the shore and was going to meet up with the yacht.
You can see the perspective here. Scroll down:
http://www.nydailynews.com/news/politics/john-kerry-chills-exclusive-nantucket-retreat-article-1.1391014
If you scroll further down it appears that boat is too small to carry the zodiac.
The Isable is 75 foot long and I can’t see where the zodiac is hauled up and stored.