United States-Flag Merchant Marine Revitalization Act of 1999 - Amends the Merchant Marine Act, 1936 to add to the list of vessels for which a capital construction fund may be established vessels that are for operation in oceangoing domestic trade between two coastal points in the United States or in support of operations conducted on the Outer Continental Shelf. 
Redefines "eligible vessel" to eliminate references to being constructed or reconstructed in the United States.  Revises the definition of "qualified vessel" to: (1) add references to such trade and operations; and (2) mandate an agreement with the Secretary of Commerce.  (Current law mandates an agreement with the Secretary of Commerce regarding fisheries vessels and with the Secretary of Transportation regarding all other vessels.) Removes the definition of "noncontiguous trade." 
Removes references to containers from provisions requiring that, in order for a withdrawal for a barge or container to be a qualified withdrawal (and except to the extent provided in regulations), the barge or container must have been constructed in the United States.  Adds containers and trailers that are part of an eligible vessel's complement to the definition of "vessel." 
Defines "foreign commerce" and "foreign trade." 
Adds as qualified withdrawals from such funds payments that reduce the principal amount of a qualified lease of a qualified vessel or container that is part of an eligible vessel's complement.  Adds references to payments to reduce the principal amount of any qualified lease to provisions regulating the tax treatment of qualified withdrawals.  Defines "qualified lease" as any lease with a term of at least five years. 
Adds the amount elected for deposit under specified provisions of the Tariff Act of 1930 to the list of amounts, the sum of which is the limit on deposits to a fund in any taxable year.  Includes that amount in the capital account.  Allows deposits in excess of the limit if a change in taxable income for a prior taxable year is such that a deposit could have been made for that prior year. 
Modifies: (1) the contents of the capital gain and ordinary income accounts; (2) the tax treatment of nonqualified withdrawals from the capital gain account; (3) requirements regarding the tax rate on nonqualified withdrawals; and (4) requirements regarding unqualified withdrawal interest payable under specified provisions of the Internal Revenue Code. 
Allows amounts in such funds to be invested in income-producing assets (including accounts receivable) approved by the Secretaries of Commerce (for fishing vessels) or Transportation (for all other vessels). 
Amends the Internal Revenue Code to deem withdrawals qualified if they are for payments that reduce the principal of a qualified lease of a qualified vessel or container that is part of an eligible vessel's complement.  Allows, if a qualified withdrawal is made from the ordinary income or capital gain accounts and used to reduce such principal, a reduction in the basis of vessels, barges, and containers owned by the person maintaining the fund. 
Adds the amount elected for deposit under specified provisions of the Tariff Act of 1930 to the list of amounts, the sum of which is the limit on deposits to a fund in any taxable year. 
Modifies the contents of the capital account. 
Allows deposits in excess of the limit if a change in taxable income for a prior taxable year is such that a deposit could have been made for that prior year. 
Modifies: (1) the contents of the capital gain and ordinary income accounts; (2) the tax treatment of nonqualified withdrawals from the capital gain account; (3) requirements regarding the tax rate on nonqualified withdrawals; and (4) requirements regarding unqualified withdrawal interest payable under specified provisions of the Code. 
Allows amounts in such funds to be invested in income-producing assets (including accounts receivable) approved by the Secretaries of Commerce (for fishing vessels) or Transportation (for all other vessels). 
Modifies requirements regarding qualified withdrawals and containers that are part of the complement of a qualified vessel. 
Links definitions in related provisions of the Merchant Marine Act, 1936 to definitions in related provisions of the Internal Revenue Code. 
Removes provisions relating to marine capital construction funds from provisions regarding the determination of the alternative minimum taxable income of a corporation. 
Amends the Tariff Act of 1930 to allow the owner or master of a vessel, documented under U.S. laws to engage in foreign or coasting trade, that has purchased equipment or repairs in a foreign country to deposit the ad valorem duty on the value of the equipment or repairs in a capital construction fund rather than paying them to the Secretary of the Treasury.
Output: United States-Flag Merchant Marine Revitalization Act of 1999