When we arrived home my wife and I were looking for a way to post comments about our trip to Egypt, We took the NCL Jade (Istanbul to Athens) and RCL Legend of the Seas (Rome-Rome)
For ports that the stay are less than 12 hours, I would go with the ship's excursions. It is because the ship would not depart until all passengers on their excursions are returned.
For Cairo, Jade docks in Alexandria over night. and it is about three hours drive to Cairo. Jade charges over US$400/person for an overnite tour and US$169/person for a one day tour with 40 people in a group.
We booked private (for two of us) tours with Ramses Tours of Alexandria (firstname.lastname@example.org) for US$95 for the day trip to Cairo and US$60 for the day tour of Alexandria. The cost includes private car, a driver, a tour guide and all admissions. The tour guide met/return us at the dock right in front of the gangway. We made the bookings on internet and paid US$ at the end of each tour plus tips to both the guide and the driver.
For the Cairo tour, we had an excellent guide, Marwan Mohamed Sayed, who is an Egyptologist. He speaks excellent English. During the long drive to Cairo, he kept us awake by giving us infos on Egyptian history, culture, geography, etc and answerd our quiries. We visited the pyramides, the Sphinx, the Egyptian Museum, etc. We also took a 10 minutes camel ride for US$30 extra. Inside the museum, Marwan was able to guide us through more exibits and faster than groups of 30-40 peoples. The tour took 12 hour (8 am - 8 pm).
Our tour guide for Alexandria was "Mohamed ally" the tour was great. We visited about six landmarks including the mammoth Alexandria library. The tour took 7 hours (8 am - 3 pm).
Hope these will be of help for you and have fun on your cruise.