As with most design-related things, I would argue that there is no "best way" to design maps either. You should really just experiment with different tools. But I'll share what worked for me (your mileage may vary).
Personally, I find that tool to use varies on my mood. Sometimes I'll do pen-and-paper sketches. Other times (especially when I want to share my designs over IM), I end up doodling in a paint program. Sometimes, I'll open up a map editor like tiled (or sometimes other poorly-written editors that have lots bugs and I wouldn't recommend to anyone like maped3 but which I have great familiarity with) and use some placeholder tile art, which I gradually refine into a real map with useful tiles (not as useful for more involved maps that are not 2D, however -- but might be a starting point to get a rough layout).
If I'm not in a terribly visual mood, I might even just open up a plain-text editor and describe an area in writing. I've occasionally found myself just plotting out an area in ASCII art. The particulars will be better sorted out when I actually feel like crafting a complete map.
Some people might enjoy using 3D modeling tools, but I personally find them too involved and time-consuming. And I don't feel this sort of encumbrance when doing 2D sketches and tilemaps. After all, these are temporaries, and world designs are likely to change after they've work into a playable prototype.
(Similarly, I probably wouldn't use a specialized prototyping tool for deciding a user interface. But I do use other options. I could draw it out by hand. Perhaps I'd scribble in a paint program. Maybe fire up a detailed mockup from the get-go. Possibly even defer the interface specifics until I have coded an unstructured but working prototype.)
However, find whatever works for you. Keep trying new things, going with what suits your current mood, and while you may never find the "best" method, you'll find something functional, and that lets you at least make steady progress.