It seems like everyone is abandoning their production of small LC filters (e.g KNH16C104DA5TS).
What is a good alternative for the simple 3 legged LC filter?
Discrete passives are probably the best bet. While not as compact as an integrated filter component, the prospects of finding alternatives in the present scarcity environment is much, much better.
The closest LC filter with 0.1uf, and 3 leads, is 490-9806-1-ND.
Please check the datasheet, and see if this item will work for you.
I appreciate your reply Rick. So a resistor and capacitor should cover the basis here? I’ll read up more on the LP filter designs.
Thank you David! Unfortunately I need SMDs. 
They will be different. Click here for some options. These are similar ones in SMD, but will have difference capacitance ratings.
Hunh… On further inspection, I’m thinking that your original part may have been mis-classified, insofar as it’s labeled as an “LC” type filter and in the EMI/RFI filter family, despite no evidence in the datasheet of any intentional L built in and what appears to be a 20dB/decade slope, which doesn’t seem consistent with the 2nd order behavior one would expect from an LC network.
In other words, whatcha had there would appear to be better classified as a feedthrough capacitor. While not as generic and multi-sourceable as plain vanilla MLCCs, they’re rather more so than integrated filter network devices, and the second part you mentioned above would indeed seem to be of close kinship.
To exposit the taxonomical road apple that we seem to have stepped in here a bit further, there also exists a thing known as an “X2Y®” capacitor, which is extremely similar to but not exactly the same as a feedthrough cap. (0.1u/0603 devices here) which we nevertheless have filed among the plain-vanilla MLCCs as of this point in time. I’d politely excoriate the trademark authorities for granting that one and the guilty marketing personnel for asking, due to the potential for confusion with safety-rated capacitors which can carry very similar-looking designations…
In any case, for EMI purposes the layout & package of any given device can have significant influence on the end result, owing to the parasitic inductance that shows up as a result. Depending on the application and whether or not the sporty feedthrough cap mentioned originally was really needed or chosen Just Because, it’s imaginable that you might be able to get by with switching to a plain old MLCC, which would probably be a best-case scenario from a procurement perspective.
Thanks Rick! Very thorough response!