I have had some crypto on exchanges longer than I'd like.
Do you really need another mt.Gox shit to take place in your life? Trusting exchanges is really bad, there may be literally very high risks associated with the exchanges holding your coins. Just move out your coins and hold only which you are trading currently.
I'm wondering what the best means of storage currently are since I haven't been paying attention much this year.
For offline/cold storage is it still a debate between paper wallets (very annoying to setup) and the ledger nano S?
It would be good if you store your coins offline. Some of the secure storage options include
[1] Buying a good hardware wallet like Trezor, Ledger or Keepkey. You can better stick to any of these 3 hard wallets.
[2] Creating a paper wallet if you are really aware what you are doing and have a basic knowledge on how a paper wallet works. Spending from a paper wallet quite often is really a very tedious job which may lose one's interest in them.
[3] Creating an offline environment for storing your coins securely. You can do this by buying a cheap laptop and never connecting them to network. Download Electrum from a online computer and securely move them to a offline one and store them. You can even create a multisig wallet so that it needs atleast 2 persons to sign the transaction to release the funds. Electrum offers a wide range of hard wallets support and you can integrate almost all the above mentioned hard wallet with your Electrum wallet. In order to track the funds, you can create a watch only wallet in any of your online PC or Mobile
I want to store these long term. However, I worry about the Ledger because it is still operated through a third-party. I also dislike paper wallets because the process is so tedious and a hassle; especially for multiple coins.
Hard Wallets would be safe until you generate the seeds yourselves. There needs to be trust among anyone doing a good job for the past years. If you don't believe anyone, better stick to the paper wallet and generate them by flipping a coin or a die. Ledger is an open source project as suggested by OmegaStarScream but the firmware itself is not an open source.