You can certainly find a decent condition shinto wakizashi for under $1000 USD. If you check the sales section you can get some remarkable deals from members.
The recent surge of "cheaper" nihonto on ebay is not to be simply ignored, while many of these wakizashi coming out of Japan are neither particularly fine, papered or in excellent condition they are for the most part genuine swords. Most have gimei, flaws or are in poor condition and the prices reflect that.
However my advice is to purchase through the reputable dealers, many of which post here, and come away without any doubts and a fine example of what you're looking for.