Is the 3DES encryption algorithm the best choice for S/MIME protocol?

Actually, the 3DES encryption algorithm was part of the original S/MIME protocol. However, 3DES -- also known as Triple DES, or the Triple Data Encryption Standard -- is based on the DES algorithm developed by an IBM team in 1974. Triple DES was originally designed to run in specialized hardware, so it's considered computationally expensive on general-purpose processors.

Because of the limitations of the key lengths used in 3DES and its poor execution on general-purpose computers,...

S/MIME eventually adopted AES as the standard for its encryption. AES, also known as Rijndael and FIPS-197, is a symmetric block cipher that can accept variable block and key lengths up to 256-bits and isn't restricted to the less secure 64-bit key lengths of 3DES. Plus, it would probably run a bit better on your server than 3DES. Because of this, it's hard to recommend using 3DES (even though it should be technically possible) because ultimately you'll be taking a giant step backward. But assuming you have a requirement due to a legacy system, I'd recommend doing some research on the Internet to find an old copy of the S/MIME protocol standard for guidance on how to integrate a 3DES encryption key into it.