The most scenic way to get to Stornoway from the mainland is from the Uig ferry on Skye to Tarbert on Harris. There's usually connecting buses at both ends.
If your coming from Glasgow, drive by Loch Lomond-Glencoe-Fort William-Glen Sheil-Lochalsh-Portree, then stay the night in Portree. Catch the ferry the next day to Tarbert.
Alternatively drive to Mallaig and take the ferry to Armadale in Skye, and stay the night in Portree.
We got the ferry from the isle of Skye to Harris and they do have tickets that allow travel around the Outer Hebrides getting you from one island to the other. We then went onto Uist and Benbecula. You do have to book in advance.
There are three ferry ports on Harris and Lewis.
At Stornoway (Lewis) going to Ullapool
At Tarbet (Harris) going to Uig on the Isle of Skye
At Leverburgh (the southern tip of Harris) going to North Uist and the Isle of Berenay.
If you're planning on hiring a car on the Island, and expect to do a lot of driving down the smaller roads, and exploring the back roads, then opt for a manual gearbox.
From experience on the island, an automatic will burn through your fuel a lot more, as the engine is constantly changing gears and wasting your precious fuel reserves.
Although there is public transport it is limited and by far the best way to get around is with you own car.