It's nice that you enjoy running and cycling.
Here's a reference for HK Island.
1. Bowen Road. This road starts from Magazine Gap Road in the Central Mid-levels to Stubbs Road Happy Valley Mid-levels. It is pretty flat and there are many people use it for jogging on weekends. Technically, a portion of Bowen Road is cycling prohibited but I saw people cycling anyway, just don't ride your bike fast.
2. Seaview Promenade. It connects Deep Water Bay to Repulse Way. It is idea for cycling as it less crowded than Bowen Road on weekends.
3. Happy Valley Racecourse. There is one trail inside that circulates the racecourse. It is convenient for people to have a morning walk before work on weekdays.
4. Victoria Park Causeway Bay. Same use as Happy Valley Racecourse.
5. Wilson Trail Stage 1. It starts at the Stanley Gap Road and ends at to Wong Nai Chung Reservoir. It is hilly but you can enjoy the scenic view along the 4.8 km trail.
You can enjoy the trail along the coast of Tsim Sha Tsui and Hung Hom. Unfortunately, part of it (In front of New World Renaissance Hotel) is closed due to construction of the extension of East Rail.
There is a cycling trail from Tai Wai to Tai Po along the Sing Moon River and Tolo Harbour. The trail continues to Shuen Wan Reservoir.
There are also cyclists cycling on New Castle Peak Road from Tuen Moon to Tusen Wan along the Gold Coast, on Route Twisk from Shek Kong to Tsuen Wan, and on Tai Mong Tsai Road from Sai Kung to Wong Sek Pier.
As for bicycles on ferries, Star Ferry allows bicycles on Tsim Sha Tsui-Wan Chai line, Central-Hung Hom Line and Wan Chai-Hung Hom Line. If you can take up the challenge, you can try to take your bike on First Ferry from Central to Mui Wo and ride your bike up South Lantau Road....