I don't think so as the AF was 2 rail DC and Lionel is 3 rail AC, at least that is my understanding. However, your best bet for a really good answer is to place this question on the "Classic Toy Trains" section of the forum. There your message will be seen by many who will know for sure.
Simon Modelling CB&Q and Wabash See my slowly evolving layout on my picturetrail site http://www.picturetrail.com/simontrains and our videos at http://www.youtube.com/user/MrCrispybake?feature=mhum
Actually old AF trains were AC as well. To be more technically accurate, both AF and Lionel had 'universal' motors which actually can work on AC or DC (I've run a 1948 vintage Lionel on DC - works fine). To run on DC you have to disconnect the whistle if present as it will blow continuously (taht's how the whistle button works - it superimposes low voltage DC on the AC track power which trips a relay in the tender).
Now for the complicated part - somewhere in the MPC era, Lionel's lower end pieces had DC motors - I have a Lionel set that has a DC power pack, and there is no rectifier or anything that would allow it to run on AC. It's strictly DC only. So the answer remains as an "it depends" - it depends on which specific Lionel equipment is being used. Also, 40 watts isn't much, especially when it comes to vintage Lionel. Add the loco, a whistle tender, smoke unit, and a couple of accessories and you're over 40 watts real quick.
Final thought - old vintage transformers might seem like a deal, but carefully inspect them. The wire and more particularly the insulation on said wire is old and may be brittle or cracked. Especially chek there it enters the transfromer body and at the plug, the two highest stressed areas. If there are any cracks or breaks in the insulation, don't een attempt to plug it in. And don;t try to open it up and replace the cord with a new one, unless you are absolutely sure you know what you are doing. 120VAC shocks are not fun an potentially lethal, or frayed insulation could result in a short that starts a fire. If you are serious about rinning vintage Lionel and AF trains, consider getting a new transformer. The new ones will have the added benefit of being UL Listed, which means they at least meet some basic safety standards as far as shock and fire hazards go.
--Randy
Modeling the Reading Railroad in the 1950's
Visit my web site at www.readingeastpenn.com for construction updates, DCC Info, and more.
Both Lionel and American Flyer transformers' output is AC. The Wattage output of them is probably different, but either brand should work with the other.
But, for a transformer this old, you need to very carefully examine the power cord for cracked insulation and replace it if necessary. One weak point of the AF transformer was the wiper that regulated the voltage output. It just slid across the windings of the transformer, which could cause it to suffer from excessive wear and intermittent contact.