You can easily do all of these ports on your own, I think it would depend on your comfort level.
I don’t think you need to do the ships excursion; the metro is clean and reliable. But you will need to walk about 25 min from port.
Check out this link: http://www.athensguide.com/athens-wa...ours/index.htm
Definitely visit Acropolis, Lycabettus Hill, and Walk around the plaka for some really cool souvenirs.
At the entrance of the Acropolis you can hire a guide. I don’t think you’ll need a guide though unless you want more insight into the site. There’s also an Athens walking tour that meets at Syntagma metro station.
Have lunch at Thanasis in the Plaka; 69 Mitropoleos, actually many of the best restaurants in the Plaka are on Mitropoleos St.
Have sandals made by the "THE POET SANDAL-MAKER OF ATHENS”. The address is at 2, Aghias Theklas St., in Monastiraki . By foot. Getting there is very easy. The store is within a walking distance from Syntagma Square (The main Square of Athens). You just walk down Ermou Street, past Kapnikarea Sq, till you reach Athenas St (on your right handside), and Monastiraki square (on your left handside). Aghias Theklas Street is the 2nd right after Athenas St. (the first being Miaouli St).
By train. If you are not in the mood of walking you can take the metro to Monastiraki Square. When you exit the station you head towards Ermou St. Aghias Theklas Street is the 2nd right after Athenas St. (the first being Miaouli St).
You can get a walking tour around 20 euros from the center of town; it’s a walkable city. The port is w/in walking distance. There’s a lot of museums, but the Palace of Diocletian is worth the visit even on a self guided tour. If you have time, take a bus ride to Trogir in the morning which is about a 30/40 min ride on the Express, and 50 on the regular local bus. It’s a beautiful town which is an UNESCO world heritage site.
I’d rent a car; the island is so beautiful. Here’s a link on how you can plan your day.
Walk around Little Venice
Take a picture in front of the windmills
If you like/love greek history, visit Delos by boat
The ship docks literally in the center of the small town. It is a five minute walk to the main street with shops and waterfront cafes. If you're interested in Greek history visit Olympia & the museum by train, otherwise it should be a pretty relaxing day.