If a person was looking to design a good place to fish in the open water for a variety of species, within an easy paddling distance of a safe launch area, you would probably design the combination of launching at Shelly Beach and fishing at Bluefish Point.
Shelly beach is very protected in pretty much any conditions. When launching, drive down the utility ramp at the Fairy Bower parking lot. Unload your kayak next to the Kiosk and drive back up the steep road.
Launch from the beach right next to the old boat ramp. If it is early there won't be anyone around. Later in the day everyone will glare at you for driving down - just act like you belong there and noone will hassle you, tho.
The area around Shelly Beach is a Marine preserve - don't cast a line until you are well and truly clear of the break or you will get in big, big trouble! http://www.raley.com/images/bluefish-nofishing.jpg
If you don't want to pay to park, after launching head right back up, out of the expensive carpark and find a spot on Bower Street. You can park for as long as you like for free! Again - if it is past dawn forget about this option.
Manly is a very safe suburb and your vehicle should be completely safe.
EDIT: The street parking around the area has been changed to 2P - if you are going to be returning later than 10:00am you'll have some issues....
While in theory one could take a left out of Shelly Beach and head up Manly Beach, most anglers do the opposite and head around to Bluefish Point, which offers Trevally, Slimy Mackerel, Australian Salmon, Snapper and YellowTail Kingfish in the right conditions.