I agree with what Rich said, and if the boat is near your house, and you have that gear, coupled with good access to both ends of all applicable hoses, it's the way to go. If not all of that is true for you, here is another way, which I have used prepping for deliveries. (BTW, if the tank is empty, this would be the time to consider installing a larger access plate.)
1) Empty the tank (which you have done), and polish that fuel, if you have the capability. If not, consider paying someone to do it. If that doesn't make financial sense due to a relatively small quantity, donate it to a farmer running diesel equipment.
2) Devise some sort of tool - a rod, coat hanger, etc. to which you can attach cheap disposable paper shop rags (see #3 below). The method of attachment doesn't matter, but changing of rags should be easy and quick. Two or more tools is helpful, and they should be semi-bendable, to allow you to reach all of the sections of the tank. The length of the tool depends on the dimensions of the tank.
3) Buy a couple of boxes of paper shop rags at the auto store or similar. They come 100 or so per box, and are disposable. How many you need depends on the size of the tank, but buy more than you think you need. They don't go bad, and can be used for other things on a boat or in a shop.
4) Use the rags, attached to the ends of the rod, to progressively wipe the gunk out of the tank. Start on the tank's "ceiling", then the sides, so the crap dropping off doesn't need to be cleaned up again. Wear gloves, and just put the used rags into a garbage bag. (This goes faster if you have a helper attaching the next rag to an unused tool, so you can just wipe, wipe, wipe.)
5) When you have it visually clean, you can spray the inside (with a flexible hose and dollar-store plant mister, or similar) with isopropyl alcohol (rubbing alcohol). Absent a sprayer, go back to the rags and douse a rag with the alcohol and wipe again. You can skip this step if you want, as the gunk is usually some combination of bacteria and algae. Alcohol will help with the former, but not so much with the latter. I use isopropyl because it is readily available and it evaporates quickly - you won't have to mop it out or drain it from the tank.
6) Use a biocide in your diesel from here on out. Opinions on biocide are as varied and conflicting as those on anchors, so do your own research. Follow the manufacturer's instructions on amount and frequency of use.
7) Change you fuel filters, regardless of whether you clean out your lines. You should clean out your lines if you can, but if you don't, good (clean) filters should keep the crud out of your injectors.
I have done this on 12 to 18 gallon tanks. It's a pain, but when you fly into the boat's location and can't bring everything you have at home, it works. I have also done in on tanks that were 60 + gallons, but in those cases the access ports were big enough to get my arm into, and I could reach the bottom of the tank while lying down on the cabin sole. It's up to you to decide which method is faster or easier. Tools, tank access, tank shape, and fuel line locations all factor in to your decision.
