Yes, the level of a skill is the sum of whatever points you have invested yourself plus any on equipment bonuses (up to the level cap). At least in the Xbox version of the game, the skill window will list the total points you have, while the detailed description will show what you have learn yourself, and equipment bonuses separately (ie is will show '(3/5) + 1').
In your example you would have level 4 of Wisdom. If you went and got Rothman's bow (as a quest reward for saving him from a troll), then you would have level 5 when the bow was equipped, but level 4 if you were fighting melee (I used Rothman's bow for quite awhile, and made sure I switched to it before turning in quests, etc). If you found another item with a Wisdom bonus (talisman of the north, etc) or put a skill point in yourself, you would still only have level 5 of the skill, until you got the battle tower and had you trainer increase the level cap for Wisdom.
