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This question is two-fold:
No. Client pays an invoice. It's up to you to calculate all costs in the invoice or pay part of them yourself. For example, I always pay PayPal's 4%, never ask the client to pay it nor I increase my price for 4%. I treat it as my running costs.
Read point 1 :)
This is really in similar to Peter's answer I realize. However...
An important factor is that some merchant accounts severely frown upon raising rates to cover their processing charges. In fact, some outright hate it.
It devalues their name in the eyes of your clients. Think about that.... You add 4% because a client wants to pay using PayPal, they then are not happy that using PayPal costs them more so they will avoid using PayPal if possible. This directly impacts PayPal's business, not yours.
In some cases, a payment processor discovering you are increasing costs for only payments using their service may take unfavorable action towards you, such as refusing to accept payments for you.
For credit cards, there are surcharges, referred to as "convenience fees", which may be only acceptable under certain circumstances: http://www.creditcards.com/credit-card-news/credit-card-convenience-fees-cost-surcharges-1280.php
All this has also been a long-standing legal battle between merchants and payment processors: https://usbneblog.wordpress.com/2013/06/18/the-reality-of-surcharging-fees-in-the-us/
You should really never ask any client to pay your processing fees. Paying the processing fee is merely the cost of doing business, as Peter answered. If you can't afford that 2-4% then your rates are just too low to begin with.
If you didn't get this specified in the original contract (you do have a contract, don't you?) then you can't reasonably add it to the invoice.
If you did specify it, or had an 'expenses' clause, then there's no reason to worry about politeness. Just add a line item that says something like
Bank Transfer Charges per contract clause x.y $10.00
If you feel that's cheeky, then you can always add a rider which says something like "Bank charges waived for payment within 7 days" which shows good will and helps with the cash flow :)
But realistically, which service you choose to use to receive payments is your choice - not the customer's. Just as if you choose to use a more expensive paper to print your invoices on.
As mentioned in the other answers, you should include the fees in your project's price. It should not be charged as extra.
But if the client requests a special payment method that is not part of your standard payment methods then yes you can ask for an extra. For example, you have a merchant account but the client still wants to use Paypal or Western Union, you can specify there will be additional charges. That is often seen on many websites of big corporations, especially with Paypal payments. One benefit of doing this is the client might decide to use your favorite payment method instead of the one with the extra charges.
But if you offer only one payment method, then no, you don't ask for transfer fees or any other fee related to this; that's part of your responsibilities to include this in your project's cost and price.
As to how to ask for the extra charges, I think this should be done during a communication before sending the invoice. You don't ask clients to calculate their own fees; you do it. Best way to do this is by asking by email "what method of payment they prefer to use" and then offer them your choices and explain the fees without extra justifications. Then prepare the invoice accordingly. This can be asked while they ask you for a quote too, before you start the project; it's fair.
If you use an online way of collecting the payments and it can be done by adding buttons (for example), then simply do as any other corporation do and add a note below the Paypal button saying something like "10% extra transfer fee applies." It doesn't matter how you say it, people are used to this and it doesn't require any justifications when there's more than one option to make a payment.
