According to the Irish civil registration indexes, there were six boys born to Harper families in (London)Derry in the 1860s. None was called Samuel, but there is one recorded just as 'male'. In most, but not all, cases, a child was registered in this way because it died fairly soon after birth without being given a name. So this 'male' Harper is unlikely to have been your Samuel, but it could be worth checking out.
You can look through the birth register index (it's only an index, so doesn't give all the details you'd like!) at the LDS pilot site.
If you want to order a birth certificate, use the application form on the GRO site at www.groireland.ie
(6 Euros each) or apply through PRONI in Belfast (I'm not sure of price in £).
If you are feeling flush, you might find it worth buying the certificates for one or two of the other Harper birth registrations for the 1860s. If the father of one of them is Robert, you might have some interesting clues - and a location - to follow up.
Apart from that, here are some ideas for further research....
Does your grandfather's marriage certificate state what Robert Harper's occupation was? If he had a trade, he might be listed in one of the trade directories published in the 19th centuries.
Does it say he was deceased? If so, check the death registers on the LDS site for Robert Harper deaths 1866 to 1892.
Does the certificate say if any Harpers were witnesses to the wedding? (If so, these were probably siblings. Look through the Irish civil registration index for their births. And, if you think they also settled in the UK, check the UK census to see if they have left behind any vital clues.
Hopefully this gives you some directions to explore.