Make it attractive to pay tax
Charles 9 has an excellent question. One must somehow make it a better idea to pay taxes than not. Naturally, appealing to ethics is unlikely to work. And removing police protection from Amazon warehouses - on the grounds that they haven't paid for such protection - seems likely to have consequences that may be even worse.
One possibility is to have a deductible tax on transactions, like a sales tax. Such taxes would only be levied on organizations not paying income tax, and would be levied at a rate making it advantageous for Amazon et al to book their corporate profits where they earn them. The difficulty is to work out the details to be less unreasonable than present tax laws.