Windsor

No, the HO/HO bus ticket does not cover Windsor. It only covers the bus route in the city - no admissions to anywhere along the route. Windsor is an hour from London.

To answer the second part of the question - you can certainly take a train both ways very easily. A boat back is a bit more problematic. There is a company called French Brothers (http://www.frenchbrothers.co.uk/pt/pt0.htm) that do local cruises around Windsor. They also do a seasonal one to Hampton Court. From there, you could catch a second boat into central London. Guessing it would take quite a while to do, though. To my knowledge, there are no direct boat services Windsor to central London.

Take a train from London's Paddington Station to Windsor, it's a 35 minutes train ride. Will have to change trains in Slough..but its simple. Slough is 5 minute train ride from Windsor. There are trains that leave several times an hour. When you get off the train in Windsor, go to your left, you will arrive at High Street with Windsor Castle across the street. As you stand there looking at the castle if you turn to your left and walk down to the second street on your left, turn and walk down and walk over the bridge and you will be in Eton. Eton is where Eton College (which is a middle and high school) for boys, the royal's and upper class send their sons. If you would turn to your right (while looking across to the castle) and follow the road down and you would reach Windsor Great Park. There you could get a fantastic view (better then you get while inside the castle walls) of the royal residents of the castle. There is the 3 mile Long Walk..which is the private road for the royal family to use to enter and exit the castle.
After touring the castle you will exit the King Henry VIII gate across the street is a great pub Horse and Groom. The road you are on after exiting the castle is Castle Hill..off Castle Hill is St. Albans Street if you walk down it you will see the Royal Mews, where the royal horses are kept, along with the royal coaches. You can have a fun day in Windsor.

And make sure you take a picture of the station sign in Slough! Friends mostly yawned (politely) at our Windsor pix (overdose of mellow ye olde quainte...), but everyone who had ever seen the original "The Office" got a big kick out of the Slough sign!