I've taken NJ Transit/SEPTA (with a bicycle) twice and Bolt once (without bicycle) since these posts.

I think NJ Transit & SEPTA will be better for you, but each has its advantages and disadvantages.

NJ Transit/SEPTA Advantages
No reservations or advance booking required - no penalty for changing schedule
Bike is on train, secure with bungee cords - don't need blankets, no concerns for bike damage
SEPTA stops in NE Philly available
NJ Transit stations available for departure, return

Rush hour trains may be faster if buses are stuck in traffic (but you may not be able to take your bike)
Run in bad weather (probably not important for a recreational trip)

Bolt Bus Advantages
Don't have policies prohibiting bicycles at rush hour
Don't need to transfer

Afternoon buses may be faster without local stops
From NYC to 30th St Philadelphia, might save $10 - both are far cheaper than Amtrak

In your case, NJ Transit & SEPTA will give you much easier access to the Torresdale SEPTA stop in NE Philly, no concerns about your bicycle, and a little more scheduling flexibility if you're able to leave after 7:00.

You can roll your bike on to the train from the platform at Penn Station, Trenton, and 30th Street (Phil), so transferring at Trenton is very easy. At Torresdale, you'll certainly have to carry your bike onto and off of the train (narrow steep stairs) and may have stair cases. SEPTA says Cornwell heights is 2.5 miles from Torresdale and is handicapped accessible, so this might be more convenient. (SEPTA also says the Claymont DE station is handicapped accessible. It is not.)

I haven't taken a bicycle on Bolt, however
* Drivers have told me it's no problem, they put it under the bus
* I did see someone with a nice looking hybrid take it on Bolt from Boston
* Years ago I took a bike on a bus (Greyhound?) with no problems; bike was 20 years old, not concerned about scratches