What are some of the best alternative programs to the Boy Scouts?
I think this article about faith-based alternatives is helpful:
The one I know the most about is the Calvinist Cadet Corps, which has roots in the Christian Reformed Church (the Dutch Reformed had problems with Baden-Powell's generic approach to religion all the way back to the earliest days of Scouting) but now contains a number of Orthodox Presbyterian and United Reformed church groups. Personally I'd love to see a major influx of PCA churches and others which have traditionally used the Boy Scouts.
For those in other denominations, the article also references the Southern Baptist Convention's Royal Ambassadors, the Assemblies of God's Royal Rangers, and the Seventh Day Adventists’ Pathfinders.
My guess is all of these groups are going to see a major influx over the next few years unless the Boy Scouts make a major change and do it quickly.