IT DEPENDS.

If the goodwill asset is considered personal goodwill from one of the shareholders, the shareholder recognizes capital gain on the sale of the asset. For instance, if a shareholder sells a business in which his or her personal relationships with clients/customers are important to the purchaser, the personal relationships are considered personal goodwill and will be taxed as capital gain to the shareholder.

If the shareholder sells the personal goodwill to the s-corporation and in return gets paid in the future for services provided to the s-corporation as a result of the goodwill, then those earnings will be ordinary income to the shareholder. For example, if the only shareholder in an s-corporation sells the personal goodwill listed above and agrees to be a shareholder/owner at the business acquiring the goodwill, the income earned by the selling shareholder at the new business will be taxed as ordinary income to the selling shareholder. 

Lastly, if the business created the goodwill, such as a license, a customer list, brand name, etc, the asset will be considered a capital asset and will be subject to capital gains tax to the s-corporation. The asset will have zero basis if it is self-created.

Please read the following article found in the Tax Adviser Journal.
https://www.thetaxadviser.com/issues/2014/may/payne-may2014.html