The stain can be an oil based wiping stain. For a deeper color use a penetrating or gel stain. For the finish I like <a href="//www.painters-toys.com/clear-wood-finishes/oil-base-varnish.html" target="_blank">McCloskey Man O'War Spar Marine Varnish</a>. I think it is still the best.
The dark streaks is from water getting into the wood behind the finish. This can be prevented by applying a small bead of paintable clear caulking where the wood and glass meet. The same water can also cause some or most of the flaking.
All clear finishes break down eventually from water and UV light. Maintenance of the finish is needed every few years. I think the marine spar varnish is easier to maintain.