Furigana really is a crutch. You'll just form a habit of glazing over the kanji if the furigana is visible. Try reading seinen mangas, even if you don't like anime. Coppelion is a real good one, that I would recommend. You can also read light novels, or "pocket books." The point is to increase your frequency of common usage words and move on to the more uncommon later.
If you prefer a more methodical approach, you can get a list, program, or card set for different kanji levels and study the On Yomi first. On Yomi are often the reading for a compound word, while the Kun Yomi are usually the kanji by itself (verbs and single character words). The advantage of this is there are often fewer On Yomi readings for each character. Also, if you don't know the word that you suspect is a Kun Yomi, you can type it into an electronic dictionary as On Yomi and just add the kana that follows.
Personally, I do both.
You can read online, like the poster above suggested, however, I would suggest finding a way that does not have furigana available in the reading.