Blair is the only remaining candidate. First, we know she has had at least one, and at most two recent sexual partners. Louis seems like a very formal and cautious person, so I can't really see him having unprotected sex. Additionally, given that Louis and Blair are in a relationship (and they therefore can anticipate having sex), they are more likely to use protection. When Chuck and Blair had sex, on the other hand, it was unplanned and spontaneous, meaning protection is unlikely to have been used. Assuming Blair has a 28-day menstrual cycle, she would be ovulating somewhere around day 14. Let's assume she and Chuck had sex on day 14 of her cycle. In that case, Blair would expect to get her period on May 21st. On May 27th, Blair would be nearly one week late. The pregnancy test was the top-most item in the garbage can, so we can assume it was taken on or around the 27th.
Let's assume that Blair took the test during the week in which she was expecting her period: day 1 to day 7 of the menstrual cycle. If May 27th is day 2 (there's no reason to take a test on the day you're expecting your period), Blair would have been ovulating on or around May 11th. If May 27th is day 7, ovulation would have occurred on or around May 6th. Thus, the most likely date of conception is between May 6th and May 11th. We know that Blair definitely had sex at least once during this time period. During this time period, Blair is most likely to have had unprotected sex on May 6th. We can be reasonably sure that she only had one partner on this date. Therefore, the only logical conclusion is that Blair is pregnant with Chuck's child.