The answer to your question partly depends on what port you left before Yokohama.
Assuming that it was a port in Japan, and assuming that your ship arrives on time, it will probably be cleared by 07:00.
The answer also partly depends on where you bought the transfer; cruise line or independent?
If the cruise line is operating the transfer, they will decide when you and 50 of your best friends will leave the terminal on the bus.
If you have an independent transfer, you will decide when your car or van will pick you up.
Bus transfers from Osanbashi Terminal at Yokohama to Haneda Airport take about 45 minutes.
Cars and vans take about 30 minutes.