I think you misunderstand. The NYT site says Jones will win by 5%, based on the current trends. Look further down the page for their margin meter and % chance of winning meter.
Top graphic shows actual votes counted at present.
There is a link embedded in that section that jumps you to the estimate further down the page..
Roy Moore leads by 6 percentage points over Doug Jones with 43 percent of precincts fully reporting. (Jump to estimate of final result)
CANDIDATE PARTY VOTES PCT.
Roy Moore
Republican
228,585 52.2%
Doug Jones
Democrat
203,064 46.4
Total Write-Ins
—
5,911 1.4
https://www.nytimes.com/elections/results/alabama-senate-special-election-roy-moore-doug-jones
I’m betting they were using the former Tuscaloosa trend in their analysis.